The Combating Terrorism Center earns high praise from counterterrorism experts as a haven for rigorous, practical scholarship on terrorism and Islamic extremism. Its researchers consider themselves to be the opposite of analysts like William Gawthrop, the FBI intelligence analyst who compared Islam to the Death Star and Mohammed to a “cult leader.” The CTC experts’ challenge, as they themselves see it, is to undo the work of Gawthrop and his allies.

“At CTC, there’s an ethos of education,” says Brian Fishman of the New America Foundation, a former research director at the Center. “When you have that, you inherently recognize that you need to illustrate that, for example, the practice of Islam around the world isn’t monolithic.”

The CTC, as it’s known, has had a partnership with the Bureau for years; all new FBI agents go through a mandatory class prepared by the Center about international terrorism. But it’s unclear how thoroughly the Bureau will allow the CTC to revamp its curriculum — especially when there has for years been a powerful strain of Islamophobic sentiment running throughout the Bureau.

After Danger Room’s investigation revealed pervasive anti-Islam sentiment within FBI professional education system, the Bureau announced in late September a “comprehensive review of all training and reference materials” related to terrorism. That review is still ongoing, although a source tells Danger Room the FBI might announce its results as early as mid-November.

A review committee is scouring over 150,000 pages of counterterrorism training material, more than 4,500 presentations and a little more than 16 hours of video, “from all FBI field offices, as well as materials utilized by the Counterterrorism and Training Divisions,” according to an FBI statement. Unnamed “non-FBI personnel with academic training in areas of Islamic studies and Arab history” are involved in the examination.

The review’s criteria for counterterrorism training is vague, according to the FBI’s statement. “Training must conform to constitutional principles and adhere to the FBI’s core values,” it says; it must be “supported with appropriate course materials”; trainers must be “knowledgeable of applicable subject material”; and that material must “facilitate further learning and professional development.”

Almost as soon as the review began, the FBI reached out to an organization it has partnered with since 2006: the CTC. Bill Braniff, a retired Army captain and Director of Practitioner Education at West Point, spent much of October in meetings at Bureau Headquarters in Washington D.C. designing what a source familiar with the process describes as “guidelines for objectionable material” to exclude from agent training.

It’s unclear whether the FBI has allowed the CTC to go further in designing a curriculum to replace the lectures Gawthrop was permitted to deliver to special agents at Quantico. All the FBI statement says about the review’s mandate is that “items determined to conflict with the guidelines will be removed from FBI training curricula.” That sounds like the reviewers will merely cull existing training material, not write new ones, though FBI spokesman Christopher Allen says their guidelines will “be used for developing curricula going forward.”

In its eight-year history, the CTC has built a reputation as a non-ideological haven for rigorous, data-driven counterterrorism research. It compiled perhaps the most thorough profile ever of the foreign fighters that flocked to Iraq, based on captured military documents. Its monthly newsletter, the CTC Sentinel, is widely read in counterterrorism circles. Not only does the CTC teach the Army’s cadets at West Point, who will have to distinguish between Muslim civilians and insurgents in warzones, it consults for state and local police — and the FBI.

“CTC has been a leader in the field in terms of the quality of analysis and academic studies that it produces,” says Daveed Gartenstein-Ross, a counterterrorism analyst at the conservative Foundation for the Defense of Democracies. “Its work has been both high caliber and also balanced, so I think it’s an appropriate institution to work to overhaul the FBI’s counterterrorism training.”

Braniff declined to comment for this story. But Fishman, who used to work with Braniff, considers him one of the CTC’s finest. “Bill is one of these people who has not published extensively,” Fishman says, “but is one of the smartest guys and one of most thoughtful people on these issues out there.”

He also has worked with the FBI for about four years, the outgrowth of a CTC partnership begun around 2006. Back then, the FBI was still adjusting to its new post-9/11 role as an intelligence agency. It turned to the CTC to design a mandatory counterterrorism course for new agents at Quantico. And it also approached the CTC to design a textbook for agents about terrorism. The result, Terrorism & Political Islam, was a 450-page textbook that the CTC compiled and distributed to FBI field offices around the country, which are in charge of teaching the textbook. Braniff edited the second edition, published in 2008, and is at work on a third, expected in 2012.

The textbook stands in stark contrast to Gawthrop’s offerings. While it studies various extremist interpretations of Islam, it does not, by and large, conflate Islam with terrorism. “[A]n individual’s likelihood of participating in Islamist violence is not a function of piety, how closely one adheres to Islamic teachings,” writes Christopher Heffelfinger, one of the book’s co-editors. Nor does the book suggest that all terrorism is Islamic; a DVD supplement contained in the back of the book even studies Israel’s ’80s-era Machteret Yehudit terrorist group.

But Terrorism & Political Islam is a compendium, with multiple authors. And some of the FBI-penned chapters that Braniff inherited contain broad generalizations for counterterrorism agents that sit uneasily with Heffelfinger’s instruction.

A section on interviewing and interrogation, for instance, written by FBI special agents Brig Barker and Molly Amman, counsels that a sample interview with a terror suspect could begin, “What do you think about the situation in Iraq?” and proceed to elicit anti-American answers. Someone with “a patriotic and pro-Western stance” might become a potential informant, they write. By contrast, someone who doesn’t support the war could “indicate the individual follows militant ideology.”

A source with first-hand knowledge of the CTC’s relationship with the Bureau described Braniff as embarrassed by the chapter, but accepted it in order to keep relations with the FBI cordial. (The chapter will be excised in the third edition of the textbook.) Those relations could be strained. On an occasion when Braniff lectured to FBI agents, Gawthrop attended the session, glowering at Braniff from the back of the room. The source said Braniff understood Gawthrop’s presence to be a warning — should the FBI grow dissatisfied with his instruction, Gawthrop would be his replacement.

That would’ve been a major shift. While new agents learned from the CTC textbook that conflating Islam with terrorism relies on “tendentious readings of Islamic history and scripture,” Gawthrop taught that America’s war with with Muslim ideology, not Muslim extremists. During his Quantico course, Gawthrop labelled average, modern-day Muslims as violent, seventh-century thugs (see the chart, above). A few months later, in New York City, he said that the struggle against al-Qaida was “irrelevant,” compared to the threat of Islam itself.

It remains to be seen if the FBI will allow the CTC to actually design its counterterrorism training exclusively, or merely allow the CTC to be among “FBI and non-FBI” personnel who “remov[e] from FBI training curricula” material deemed objectionable. Accordingly, it’s difficult to tell if the FBI has finally made up its mind on the relationship between Islam and terrorism — or if the CTC will make the bureau’s mind up for it.